There is an option to ignore timestamps in an "atomic" way, so that you do not have trawl through all of the column mappings looking for timestamp columns.

All that you should need to do is unset MappingOptions.IncludeTimestamps in the first argument to EngineDataCompareOptions (if it is set you can use an XOR operator, for instance in C# MappingOptions.Default ^ MappingOptions.IncludeTimestamps)

In the data compare engine, timestamps can only be compared and the synchronization will ignore them anyway. For this reason, the setting should only affect any display of the data diferences, but not the actual script.